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average(FORMAT/GQ) for vcfstats #1941

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4 changes: 2 additions & 2 deletions misc/plot-vcfstats
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Original file line number Diff line number Diff line change
Expand Up @@ -212,7 +212,7 @@ sub parse_params
{
id=>'PSC',
header=>'PSC, Per-sample counts',
exp=>"# PSC\t[2]id\t[3]sample\t[4]nRefHom\t[5]nNonRefHom\t[6]nHets\t[7]nTransitions\t[8]nTransversions\t[9]nIndels\t[10]average depth\t[11]nSingletons\t[12]nHapRef\t[13]nHapAlt\t[14]nMissing"
exp=>"# PSC\t[2]id\t[3]sample\t[4]nRefHom\t[5]nNonRefHom\t[6]nHets\t[7]nTransitions\t[8]nTransversions\t[9]nIndels\t[10]average depth\t[11]nSingletons\t[12]nHapRef\t[13]nHapAlt\t[14]nMissing\t[15]average genotype quality"
},
{
id=>'PSI',
Expand Down Expand Up @@ -672,7 +672,7 @@ sub parse_vcfstats1
for my $b (keys %{$dat{$a}})
{
# Merging multiple vcfstats files. Honestly, this is quite hacky.
if ( !exists($$opts{dat}{$a}{$b}) ) { $$opts{dat}{$a}{$b} = $dat{$a}{$b}; next; } # copy all, first occurance
if ( !exists($$opts{dat}{$a}{$b}) ) { $$opts{dat}{$a}{$b} = $dat{$a}{$b}; next; } # copy all, first occurence

if ( $a eq 'ID' ) { merge_id($opts,$$opts{dat}{$a},$dat{$a},$b); }
elsif ( ref($dat{$a}{$b}) ne 'ARRAY' ) { $$opts{dat}{$a}{$b} += $dat{$a}{$b} unless $b eq 'number of samples:'; } # SN, Summary numbers, do not sum sample counts
Expand Down
46 changes: 42 additions & 4 deletions vcfstats.c
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Original file line number Diff line number Diff line change
Expand Up @@ -97,12 +97,13 @@ typedef struct
int *insertions, *deletions, m_indel; // maximum indel length
int in_frame, out_frame, na_frame, in_frame_alt1, out_frame_alt1, na_frame_alt1;
int subst[15];
int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl;
int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl, *smpl_ngq;
int *smpl_hapRef, *smpl_hapAlt, *smpl_missing;
int *smpl_ins_hets, *smpl_del_hets, *smpl_ins_homs, *smpl_del_homs;
int *smpl_frm_shifts; // not-applicable, in-frame, out-frame
vaf_t vaf, *smpl_vaf; // total (INFO/AD) and per-sample (FMT/VAF) VAF distributions
unsigned long int *smpl_dp;
unsigned long int *smpl_gq;
idist_t dp, dp_sites;
int nusr;
user_stats_t *usr;
Expand Down Expand Up @@ -513,6 +514,8 @@ static void init_stats(args_t *args)
stats->smpl_dp = (unsigned long int *) calloc(args->files->n_smpl,sizeof(unsigned long int));
stats->smpl_ndp = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_sngl = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_gq = (unsigned long int *) calloc(args->files->n_smpl,sizeof(unsigned long int));
stats->smpl_ngq = (int *) calloc(args->files->n_smpl,sizeof(int));
if ( has_fmt_ad )
stats->smpl_vaf = (vaf_t*) calloc(args->files->n_smpl,sizeof(vaf_t));
#if HWE_STATS
Expand Down Expand Up @@ -599,6 +602,8 @@ static void destroy_stats(args_t *args)
free(stats->smpl_indels);
free(stats->smpl_dp);
free(stats->smpl_ndp);
free(stats->smpl_gq);
free(stats->smpl_ngq);
free(stats->smpl_sngl);
free(stats->smpl_vaf);
idist_destroy(&stats->dp);
Expand Down Expand Up @@ -943,6 +948,26 @@ static inline void update_vaf(vaf_t *smpl_vaf, bcf1_t *line, int ial, float vaf)
else smpl_vaf->indel[idx]++;
}

static inline int calc_sample_genotype_quality(args_t *args, int ismpl, bcf_fmt_t *gq_fmt_ptr)
{
if ( gq_fmt_ptr )
{
#define BRANCH_INT(type_t,missing,vector_end) { \
type_t *ptr = (type_t *) (gq_fmt_ptr->p + gq_fmt_ptr->size*ismpl); \
if ( *ptr==missing || *ptr==vector_end ) return -1; \
return *ptr; \
}
switch (gq_fmt_ptr->type) {
case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, gq_fmt_ptr->type); exit(1); break;
}
#undef BRANCH_INT
}
return -1;
}

static inline int calc_sample_depth(args_t *args, int ismpl, bcf_fmt_t *ad_fmt_ptr, bcf_fmt_t *dp_fmt_ptr)
{
if ( dp_fmt_ptr )
Expand Down Expand Up @@ -1095,6 +1120,7 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
bcf_fmt_t *gt_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"GT");
bcf_fmt_t *ad_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"AD");
bcf_fmt_t *dp_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"DP");
bcf_fmt_t *gq_fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"GQ");

int is;
for (is=0; is<args->files->n_smpl; is++)
Expand Down Expand Up @@ -1140,6 +1166,17 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
update_vaf(&stats->smpl_vaf[is],line,jal,(float)jad/dp);
}
}

// Determine genotype quality
if ( gq_fmt_ptr )
{
int gq = calc_sample_genotype_quality(args,is,gq_fmt_ptr);
if ( gq >= 0 )
{
stats->smpl_ngq[is]++;
stats->smpl_gq[is] += gq;
}
}
}
if ( args->n_nref==1 ) stats->smpl_sngl[args->i_nref]++;

Expand Down Expand Up @@ -1753,17 +1790,18 @@ static void print_stats(args_t *args)
{
printf("# PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels.\n");
printf("# PSC\t[2]id\t[3]sample\t[4]nRefHom\t[5]nNonRefHom\t[6]nHets\t[7]nTransitions\t[8]nTransversions\t[9]nIndels\t[10]average depth\t[11]nSingletons"
"\t[12]nHapRef\t[13]nHapAlt\t[14]nMissing\n");
"\t[12]nHapRef\t[13]nHapAlt\t[14]nMissing\t[15]average genotype quality\n");
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
for (i=0; i<args->files->n_smpl; i++)
{
float dp = stats->smpl_ndp[i] ? stats->smpl_dp[i]/(float)stats->smpl_ndp[i] : 0;
printf("PSC\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%.1f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i],
float gq = stats->smpl_ngq[i] ? stats->smpl_gq[i]/(float)stats->smpl_ngq[i] : 0;
printf("PSC\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%.1f\t%d\t%d\t%d\t%d\t%.1f\n", id,args->files->samples[i],
stats->smpl_homRR[i], stats->smpl_homAA[i], stats->smpl_hets[i], stats->smpl_ts[i],
stats->smpl_tv[i], stats->smpl_indels[i],dp, stats->smpl_sngl[i], stats->smpl_hapRef[i],
stats->smpl_hapAlt[i], stats->smpl_missing[i]);
stats->smpl_hapAlt[i], stats->smpl_missing[i], gq);
}
}

Expand Down